Archive for February, 2009

The OBI winter workshop 2009

Vancouver skyline at night
Image by istargazer via Flickr

The OBI winter workshop 2009 has just been held in Vancouver. This was the first of the 2009 bi-annual face-to-face workshops concerned with the development of the ontology for biomedical investigations. The first session, on the first day, covered some administration and developmental policy issues;

Namespace –  should other communities who wish to integrate with OBI retain their namespace within OBI or loose it and gain an OBI one instead? The general consensus was that there should be only one namespace within OBI and that the source of the term/community should be described in the annotation property of each class.

Defined classes – a general development policy is that classes should not be asserted under defined classes (classes with Necessary and Sufficient conditions) this is to avoid multiple inheritance and to allow the reasoner to infer the hierarchy.

Quick ID – I presented the current status of the Quick ID policy to allow rapid term submission to the ontology. The documentation is still in a draft stage and will change, available from here.

Quick term – similar to the quick id process but concerns submission of classes which are composites (intersection of) classes that exist across multiple resources.


Several people presented use-cases on how they are either using or intend to make use of OBI.  James presented  a talk on how Genepattern software would like to use OBI. Bjoern presented how he would like to use OBI for the immune epitope database (IEDB) and Jennifer outlined potential for the CEBS. This was very interesting and encouraging that there is definitely a demand for OBI and pressure to release something.

The remaining sessions were concerned with specific branch development describing important classes that exist and any issues that were outstanding that required a broader impact from the consortium, in order to reach a conclusion. I presented reports on both the instrument branch and the relations branch status.

On the final day we dealt with the OBI manuscript, incorporating the use-cases that were presented and assigning sections to individuals for completion and the different flavours of OBI releases that our users would require. We finished with presentations from NCBO Bioportal 2.0 demonstrating new features and soliciting feedback, and from Larisa on the robot scientist which uses there own ontology for experiments to drive the robot.

All in all it was a very productive, but tiring workshop which provided the ground work for further OBI development and work on the manuscript, between now and the next workshop  Summer 2009 OBI workshop (back2back with 2nd OBO Foundry workshop), EBI, Cambridge, UK, June 2-6, 2009 (OBO Foundry 7-8; OBI 9-12)

For a full outline of the agenda (now incorporated with action items) see here.

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